As an important part of ecological remediation technology for eutrophication water, bio-rack wetland has a good development potential, and the keys to its application are selecting the appropriate plant species and maintaining a high sewage purification capacity. At present, there are few researches on microbial community structure and composition and changes of dominant population in root system of bio-rack wetland. In this paper, the mi-crobial diversity of different roots in Thalia dealbata bio-rack wetland was analyzed through PCR-DGGE. The re-sults showed that, rotted roots and yellow root had a high similarity in microbial populations, while the young rootand yellow root, rotted roots had a low similarity. The microbial species of rotted roots were abundant, but relativelyyoung root had few. Clavibacter sp., Clostridium sp., Mesoflavibacter, Brevundimonas sp. and Chromobacterium sp.played an important role in the removal of contaminant for bio-rack wetland. The research results have a certain reference value and theoretical significance for the application of bio-rack wetland to purify the water body.